Job ID = 6368381 SRX = SRX495060 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:22:21 prefetch.2.10.7: 1) Downloading 'SRR1198592'... 2020-06-16T00:22:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:25:33 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:25:33 prefetch.2.10.7: 1) 'SRR1198592' was downloaded successfully Read 19076562 spots for SRR1198592/SRR1198592.sra Written 19076562 spots for SRR1198592/SRR1198592.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:14 19076562 reads; of these: 19076562 (100.00%) were unpaired; of these: 3277970 (17.18%) aligned 0 times 13417272 (70.33%) aligned exactly 1 time 2381320 (12.48%) aligned >1 times 82.82% overall alignment rate Time searching: 00:03:14 Overall time: 00:03:14 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 5714309 / 15798592 = 0.3617 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:33:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495060/SRX495060.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495060/SRX495060.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495060/SRX495060.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495060/SRX495060.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 09:33:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:33:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:33:33: 1000000 INFO @ Tue, 16 Jun 2020 09:33:39: 2000000 INFO @ Tue, 16 Jun 2020 09:33:44: 3000000 INFO @ Tue, 16 Jun 2020 09:33:49: 4000000 INFO @ Tue, 16 Jun 2020 09:33:54: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:33:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495060/SRX495060.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495060/SRX495060.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495060/SRX495060.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495060/SRX495060.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 09:33:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:33:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:33:59: 6000000 INFO @ Tue, 16 Jun 2020 09:34:04: 1000000 INFO @ Tue, 16 Jun 2020 09:34:05: 7000000 INFO @ Tue, 16 Jun 2020 09:34:11: 2000000 INFO @ Tue, 16 Jun 2020 09:34:11: 8000000 INFO @ Tue, 16 Jun 2020 09:34:16: 9000000 INFO @ Tue, 16 Jun 2020 09:34:17: 3000000 INFO @ Tue, 16 Jun 2020 09:34:22: 10000000 INFO @ Tue, 16 Jun 2020 09:34:22: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:34:22: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:34:22: #1 total tags in treatment: 10084283 INFO @ Tue, 16 Jun 2020 09:34:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:34:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:34:23: #1 tags after filtering in treatment: 10084283 INFO @ Tue, 16 Jun 2020 09:34:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:34:23: #1 finished! INFO @ Tue, 16 Jun 2020 09:34:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:34:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:34:23: #2 number of paired peaks: 755 WARNING @ Tue, 16 Jun 2020 09:34:23: Fewer paired peaks (755) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 755 pairs to build model! INFO @ Tue, 16 Jun 2020 09:34:23: start model_add_line... INFO @ Tue, 16 Jun 2020 09:34:23: 4000000 INFO @ Tue, 16 Jun 2020 09:34:23: start X-correlation... INFO @ Tue, 16 Jun 2020 09:34:23: end of X-cor INFO @ Tue, 16 Jun 2020 09:34:23: #2 finished! INFO @ Tue, 16 Jun 2020 09:34:23: #2 predicted fragment length is 219 bps INFO @ Tue, 16 Jun 2020 09:34:23: #2 alternative fragment length(s) may be 219 bps INFO @ Tue, 16 Jun 2020 09:34:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495060/SRX495060.05_model.r INFO @ Tue, 16 Jun 2020 09:34:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:34:24: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:34:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495060/SRX495060.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495060/SRX495060.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495060/SRX495060.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495060/SRX495060.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 09:34:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:30: 5000000 INFO @ Tue, 16 Jun 2020 09:34:34: 1000000 INFO @ Tue, 16 Jun 2020 09:34:36: 6000000 INFO @ Tue, 16 Jun 2020 09:34:40: 2000000 INFO @ Tue, 16 Jun 2020 09:34:42: 7000000 INFO @ Tue, 16 Jun 2020 09:34:45: 3000000 INFO @ Tue, 16 Jun 2020 09:34:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:34:48: 8000000 INFO @ Tue, 16 Jun 2020 09:34:51: 4000000 INFO @ Tue, 16 Jun 2020 09:34:55: 9000000 INFO @ Tue, 16 Jun 2020 09:34:56: 5000000 INFO @ Tue, 16 Jun 2020 09:34:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495060/SRX495060.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:34:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495060/SRX495060.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:34:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495060/SRX495060.05_summits.bed INFO @ Tue, 16 Jun 2020 09:34:59: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2815 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:35:01: 10000000 INFO @ Tue, 16 Jun 2020 09:35:02: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:35:02: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:35:02: #1 total tags in treatment: 10084283 INFO @ Tue, 16 Jun 2020 09:35:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:35:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:35:02: #1 tags after filtering in treatment: 10084283 INFO @ Tue, 16 Jun 2020 09:35:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:35:02: #1 finished! INFO @ Tue, 16 Jun 2020 09:35:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:35:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:35:02: 6000000 INFO @ Tue, 16 Jun 2020 09:35:02: #2 number of paired peaks: 755 WARNING @ Tue, 16 Jun 2020 09:35:02: Fewer paired peaks (755) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 755 pairs to build model! INFO @ Tue, 16 Jun 2020 09:35:02: start model_add_line... INFO @ Tue, 16 Jun 2020 09:35:03: start X-correlation... INFO @ Tue, 16 Jun 2020 09:35:03: end of X-cor INFO @ Tue, 16 Jun 2020 09:35:03: #2 finished! INFO @ Tue, 16 Jun 2020 09:35:03: #2 predicted fragment length is 219 bps INFO @ Tue, 16 Jun 2020 09:35:03: #2 alternative fragment length(s) may be 219 bps INFO @ Tue, 16 Jun 2020 09:35:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495060/SRX495060.10_model.r INFO @ Tue, 16 Jun 2020 09:35:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:35:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:35:07: 7000000 INFO @ Tue, 16 Jun 2020 09:35:13: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:35:18: 9000000 INFO @ Tue, 16 Jun 2020 09:35:23: 10000000 INFO @ Tue, 16 Jun 2020 09:35:24: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:35:24: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:35:24: #1 total tags in treatment: 10084283 INFO @ Tue, 16 Jun 2020 09:35:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:35:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:35:24: #1 tags after filtering in treatment: 10084283 INFO @ Tue, 16 Jun 2020 09:35:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:35:24: #1 finished! INFO @ Tue, 16 Jun 2020 09:35:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:35:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:35:24: #2 number of paired peaks: 755 WARNING @ Tue, 16 Jun 2020 09:35:24: Fewer paired peaks (755) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 755 pairs to build model! INFO @ Tue, 16 Jun 2020 09:35:24: start model_add_line... INFO @ Tue, 16 Jun 2020 09:35:25: start X-correlation... INFO @ Tue, 16 Jun 2020 09:35:25: end of X-cor INFO @ Tue, 16 Jun 2020 09:35:25: #2 finished! INFO @ Tue, 16 Jun 2020 09:35:25: #2 predicted fragment length is 219 bps INFO @ Tue, 16 Jun 2020 09:35:25: #2 alternative fragment length(s) may be 219 bps INFO @ Tue, 16 Jun 2020 09:35:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495060/SRX495060.20_model.r INFO @ Tue, 16 Jun 2020 09:35:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:35:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:35:28: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:35:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495060/SRX495060.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:35:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495060/SRX495060.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:35:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495060/SRX495060.10_summits.bed INFO @ Tue, 16 Jun 2020 09:35:40: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1642 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:35:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:36:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495060/SRX495060.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:36:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495060/SRX495060.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:36:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495060/SRX495060.20_summits.bed INFO @ Tue, 16 Jun 2020 09:36:00: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (904 records, 4 fields): 3 millis CompletedMACS2peakCalling